Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells

Sepsis is a life-threatening syndrome causing thousands of deaths yearly worldwide. Sepsis is a result of infection and could lead to systemic inflammatory responses and organ failures. Additionally, blood cells, as the main cells in the immune systems, could be also affected by sepsis. Here, we have used different network analysis approaches, including Weighted Gene Co-expression Network Analysis (WGCNA), Protein-Protein Interaction (PPI), and gene regulatory network, to dissect system-level response to sepsis by the main white blood cells. Gene expression profiles of Neutrophils (NTs), Dendritic Cells (DCs), and Peripheral Blood Mononuclear Cells (PBMCs) that were exposed to septic plasma were obtained and analyzed using bioinformatics approaches. Individual gene expression matrices and the list of differentially expressed genes (DEGs) were prepared and used to construct several networks. Consequently, key regulatory modules and hub genes were detected through network analysis and annotated through ontology analysis extracted from DAVID database. Our results showed that septic plasma affected the regulatory networks in NTs, PBMCs more than the network in DCs. Gene ontology of DEGs revealed that signal transduction and immune cells responses are the most important biological processes affected by sepsis. On the other hand, network analysis detected modules and hub genes in each cell types. It was found that pathways involved in immune cells, signal transduction, and apoptotic processes are among the most affected pathways in the responses to sepsis. Altogether, we have found several hub genes including ADORA3, CD83 CDKN1A, FFAR2, GNAQ, IL1B, LTB, MAPK14, SAMD9L, SOCS1, and STAT1, which might specifically respond to sepsis infection. In conclusion, our results uncovered the system-level responses of the main white blood cells to sepsis and identified several hub genes with potential applications for therapeutic and diagnostic purposes.